Oryza sativa Japonica Group vs Cynara cardunculus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza sativa Japonica GroupCynara cardunculus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 156,711 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 344,183,615 out of 375,049,285
Covered: 30,865,670 out of 375,049,285

Uncovered: 15,151,797 out of 34,424,450
Matches: 12,354,976 out of 34,424,450
Mismatches: 6,454,543 out of 34,424,450
Insertions: 463,134 out of 34,424,450
Identity over aligned base-pairs: 64.1%

Cynara cardunculus

Uncovered: 692,197,297 out of 724,667,265
Covered: 32,469,968 out of 724,667,265

Uncovered: 11,587,822 out of 32,068,562
Matches: 13,330,839 out of 32,068,562
Mismatches: 6,738,258 out of 32,068,562
Insertions: 411,643 out of 32,068,562
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 156,711 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,119
5.5 kb
10 bp - 100 bp
29,706
2.1 Mb
10,109
698.4 kb
100 bp - 1 kb
119,678
36.1 Mb
37,421
14.0 Mb
1 kb - 10 kb
6,207
9.3 Mb
16,172
32.3 Mb
10 kb - 100 kb
1
10.3 kb
30
376.8 kb